[Cod-bugs] Micro-ED structures with high R_factors could not be deposited to COD as they are

[ohnishi.yusuke.corefc at osaka-u.ac.jp]

Dear Andrius,

I appreciate for your coorporation.

Could you please send me the values of _refine_ls_R_factor_gt and
_refine_ls_wR_factor_ref data items of the aforementioned CIF
depositions?

The values are below.

ID 3000620
_refine_ls_R_factor_gt           0.1807
_refine_ls_wR_factor_ref         0.4132

ID 3000621
_refine_ls_R_factor_gt            0.1112
_refine_ls_wR_factor_ref         0.3086

ID 3000622
_refine_ls_R_factor_gt            0.1336
_refine_ls_wR_factor_ref         0.3493

ID 3000623
_refine_ls_R_factor_gt            0.1623
_refine_ls_wR_factor_ref         0.4271

ID 3000624
_refine_ls_R_factor_gt            0.1612
_refine_ls_wR_factor_ref         0.4132

Best regards,
Yusuke


________________________________
差出人: Andrius Merkys <andrius.merkys at gmail.com>
送信日時: 2025年10月6日 21:14
宛先: 大西　裕介 <ohnishi.yusuke.corefc at osaka-u.ac.jp>
CC: 中根　崇智 <tnakane.protein at osaka-u.ac.jp>; cod-bugs at ibt.lt <cod-bugs at ibt.lt>
件名: Re: [Cod-bugs] Micro-ED structures with high R_factors could not be deposited to COD as they are

Dear Yusuke,

On 2025-10-06 14:53, ohnishi.yusuke.corefc at osaka-u.ac.jp wrote:
> I am Yusuke Ohnishi at the University of Osaka, Japan.
>
> We deposited 5 entries to COD (ID: 3000620~3000624).
> We had to comment out _refine_ls_R_factor_gt and
> _refine_ls_wR_factor_ref items; otherwise the Web interface did not
> accept the depositions.
> Could you please uncomment these lines on the server?

Could you please send me the values of _refine_ls_R_factor_gt and
_refine_ls_wR_factor_ref data items of the aforementioned CIF
depositions? I assume you have commented out these data items using '#'
symbol as is usual in CIF syntax, however, our software filters out CIF
comments. As a result, I cannot see these data items in the deposited files.

> They are MicroED structures refined only kinematically.
> Thus, traditional X-ray crystallography thresholds are not adequate.

Thank you, we are aware of this, and are in the process of lowering the
thresholds for MicroED structures.

Best wishes,
Andrius Merkys

--
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7
LT-10257 Vilnius, Lithuania

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